rs12646447

Variant names:

• chr4-110778170-T-C
• rs12646447

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.155 in 152,170 control chromosomes in the GnomAD database, including 2,447 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (2447 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.404
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23561 AN: 152050 Hom.: 2442 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.163

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.155 AC: 23579 AN: 152170 Hom.: 2447 Cov.: 32 AF XY: 0.163 AC XY: 12106 AN XY: 74380

African (AFR) AF: 0.118 AC: 4916 AN: 41508

American (AMR) AF: 0.221 AC: 3370 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1059 AN: 3472

East Asian (EAS) AF: 0.502 AC: 2583 AN: 5150

South Asian (SAS) AF: 0.129 AC: 620 AN: 4818

European-Finnish (FIN) AF: 0.152 AC: 1614 AN: 10604

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8997 AN: 68020

Other (OTH) AF: 0.164 AC: 346 AN: 2116

Alfa AF: 0.140 Hom.: 3050

Bravo AF: 0.159

Asia WGS AF: 0.234 AC: 814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.60
PhyloP100		-0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12646447; hg19: chr4-111699326;